21 December 2022 0 762 Report

Hello

How to perform community network analysis using GROMACS trajectory

Thank you so much

More Amnah Alalmaie's questions See All
AWH accelerated sampling?

Dear all, The complex I am trying to simulate has protein ( 10 chains), DNA, and RNA I ran the simulation for 2 us so far but the biological event I want to observe requires a very long MD...

01 June 2021 1,556 1 View

Modelling missing nt in R-loop?

Hi I would like to MD simulate a CRISPR cryo-EM- structure. But only a small region of the R-loop was observed. I want to simulate the R-loop formation. How to model the missing part of the...

21 February 2021 6,025 0 View

PME calculation on a GPU GROMACS?

Hi all I used the following script to run the simulation but for some reason, I was not able to assign GPU to do the PME calculation? How to do that? The size of the system is huge (600.000...

14 January 2021 7,654 1 View

Optimizing GPU performance on GROMACS ?

Hi My system I am trying to simulate has 600.000 atoms. I want to simulate for 1 us I am using a supercomputer to run the simulation with tesla K80 GPUs. I am using 1 node and a total of 28 core...

08 January 2021 4,903 1 View

Terminal 5' phosphate in DNA simulation using AMBER FF in Gromacs?

How to add a new termini database entries in amber FF for phosphorylated at 5'- and 3'-termini of DNA? Pdb2gmx is not able to covert pdb to gro files could you please help me?

22 September 2020 8,562 7 View

Solubility of PEG epoxide?

hello Is polyethlene glycol ( 5000 D) soluble in aceton and ethanol?

12 November 2018 2,216 1 View

Adding chromophore to PEGylation reagent?

PEG does not have chromophore do you know how to add a chromphore to make it detectable by UV detector? what is the chemistry behind that can anyone help me with that thank you

10 November 2018 4,743 1 View

Solubility of PEG epoxide?

hello Is polyethlene glycol ( 5000 D) soluble in aceton and ethanol?

10 November 2018 9,599 1 View

Effect of Gelatin on Mice?

could you please provide me with some articles that done experiments on mice by using plain Gelatin? I want to study the effect of plain gelatin on mice

09 October 2018 9,485 0 View

MTT incubation time?

Hello The standard time in our lab is 4 hrs for MCF-7 but the goal of my experiment is to study the effect of assay? The standard time in our lab is 4 hrs for MCF-7 but the goal of my...

03 April 2018 3,863 4 View

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